Ontology highlight
ABSTRACT:
PROVIDER: PRJNA716814 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14072772_1.fastq.gz | Fastqsanger.gz | |||
| SRR14072772_2.fastq.gz | Fastqsanger.gz | |||
| SRR14072773_1.fastq.gz | Fastqsanger.gz | |||
| SRR14072773_2.fastq.gz | Fastqsanger.gz | |||
| SRR14072774_1.fastq.gz | Fastqsanger.gz |
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Project description:Perturbed intestinal epithelial homeostasis demonstrated as decreased Lgr5+ intestinal stem cells (Lgr5 ISCs) and increased secretory lineages were observed in our study where Lkb1 was specfically deleted in Lgr5 ISCs using Lgr5-EGFP-creERT2 (Tamoxifen) deletor. To gain mechanistic insight how Lkb1 maintains intestinal epithelial stem cell homeostasis, Lkb1 deficient ISCs (Lgr5-high cells) and progenitors (Lgr5-low cells) are isolated by flow cytometry and profiled by RNA sequencing to compare with controls (Lkb1 wild type ISCs and progenitors).
2020-02-29 | E-MTAB-6501 | biostudies-arrayexpress
Project description:Biliary epithelial cells (BECs) form bile ducts in the liver, and are facultative liver stem cells that establish a ductular reaction (DR) to support liver regeneration following injury. Liver damage induces periportal LGR5+ putative liver stem cells which can form BEC-like organoids, suggesting RSPO-LGR4/5-mediated WNT/β-catenin activity is important for a DR. We addressed the roles for this and other signaling pathways in a DR by performing a focused CRISPR-based loss-of-function screen in BEC-like organoids, followed by in vivo validation and single-cell RNA sequencing. We found BECs lack and do not require LGR4/5-mediated WNT/β-Catenin signaling during DR, while YAP and mTORC1 signaling are required for this process. Upregulation of LGR5/AXIN2 is required in hepatocytes to enable their regenerative capacity in response to injury. Together, these data highlight heterogeneity within the BEC pool and delineate signaling pathways involved.
2018-08-27 | GSE111269 | GEO
Project description:Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes. Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2). Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis. mRNA profiles of Axin2+ and Axin2- cells from uninjured adult mouse liver were analysed by deep sequencing, in triplicate, using Illumina HiSeq 2000.
2015-08-07 | E-GEOD-68806 | biostudies-arrayexpress
Project description:The small intestine is a rapidly proliferating organ that is maintained by a small population of Lgr5-expressing intestinal stem cells (ISCs). However, several Lgr5-negative ISC populations have been identified, and this remarkable plasticity allows the intestine to rapidly respond to both the local environment and to damage. The mediators of such plasticity are still largely unknown. Using intestinal organoids and mouse models, we show that upon ribosome impairment (driven by Rptor deletion, amino acid starvation, or low dose cyclohexamide treatment) ISCs gain an Lgr5-negative, fetal-like identity. This is accompanied by a rewiring of metabolism. Our findings suggest that the ribosome can act as a sensor of nutrient availability, allowing ISCs to respond to the local nutrient environment. Mechanistically, we show that this phenotype requires the activation of ZAKɑ, which in turn activates YAP, via SRC. Together, our data reveals a central role for ribosome dynamics in intestinal stem cells, and identify the activation of ZAKɑ as a critical mediator of stem cell identity.
2022-06-13 | PXD033122 | Pride
Project description:Gene inactivation of the orphan G protein-coupled receptor Lgr4, a paralog of the epithelial stem cell marker Lgr5, results in 50% decrease of epithelial cell proliferation and 80% reduction in terminal differentiation of Paneth cells in postnatal mouse intestinal crypts. When cultured ex vivo, Lgr4-deficient crypts or progenitors, but not Lgr5-deficient progenitors, die rapidly with dramatic downregulation of stem cell markers and Wnt target genes, including Lgr5. Partial rescue of this phenotype is achieved by LiCl addition to the culture medium, but not by Wnt agonists. Our results identify Lgr4 as a permissive factor of the Wnt pathway in the intestine and, as such, as a potential target for intestinal cancer therapy. Microarray hybridization was performed on LGR4 KO intestinal crypts at day 0, day 0.5 and day 1 versus wild-type crypts. The effects of LiCl treatment on LGR4 KO crypts at day1 versus control cells were investigated. After amplification and labelling, sample pairs were hybridized onto Mouse Exonic Evidence Based Oligonucleotide (MEEBO) arrays containing on average 38784 mouse 70mer oligonucleotide probes (Stanford University, US). Hybridizations were replicated with dye swap.
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Project description:We used unbiased whole genome bisulfite sequencing (WGBS) to identify DNA methylation changes in the intestinal stem cells (ISCs) or their progeny during the suckling period of mouse colon development. Lgr5-EGFP mice were used to identify ISC populations in the colons. WGBS were performed using EGFP labeled Lgr5+ ISCs and epithelial cell adhesion molecule (EpCAM) labeled epithelial cells isolated at the beginning and end of the suckling period (postnatal day 0-P0 and P21).
2015-08-25 | E-GEOD-58532 | biostudies-arrayexpress
Project description:Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes. Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2). Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis.
2015-08-07 | GSE68806 | GEO
Project description:Intestinal epithelial stem cells (ISCs) are the focus of recent intense study. Current in vitro models rely on supplementation with the Wnt agonist R-spondin1 to support robust growth, ISC self-renewal, and differentiation. Intestinal subepithelial myofibroblasts (ISEMFs) are important supportive cells within the ISC niche. We hypothesized that co-culture with ISEMF enhances the growth of ISCs in vitro and allows for their successful in vivo implantation and engraftment. ISC-containing small intestinal crypts, FACS-sorted single ISCs, and ISEMFs were procured from C57BL/6 mice. Crypts and single ISCs were grown in vitro into enteroids, in the presence or absence of ISEMFs. ISEMFs enhanced the growth of intestinal epithelium in vitro in a proximity-dependent fashion, with co-cultures giving rise to larger enteroids than monocultures. Co-culture of ISCs with supportive ISEMFs relinquished the requirement of exogenous R-spondin1 to sustain long-term growth and differentiation of ISCs. Mono- and co-cultures were implanted subcutaneously in syngeneic mice. Co-culture with ISEMFs proved necessary for successful in vivo engraftment and proliferation of enteroids; implants without ISEMFs did not survive. ISEMF whole transcriptome sequencing and qPCR demonstrated high expression of specific R-spondins, well-described Wnt agonists that supports ISC growth. Specific non-supportive ISEMF populations had reduced expression of R-spondins. The addition of ISEMFs in intestinal epithelial culture therefore recapitulates a critical element of the intestinal stem cell niche and allows for its experimental interrogation and biodesign-driven manipulation. Two samples of intestinal subepithelial myofibroblasts were used in this study.
2013-12-20 | E-GEOD-52402 | biostudies-arrayexpress
Project description:Gene inactivation of the orphan G protein-coupled receptor Lgr4, a paralog of the epithelial stem cell marker Lgr5, results in 50% decrease of epithelial cell proliferation and 80% reduction in terminal differentiation of Paneth cells in postnatal mouse intestinal crypts. When cultured ex vivo, Lgr4-deficient crypts or progenitors, but not Lgr5-deficient progenitors, die rapidly with dramatic downregulation of stem cell markers and Wnt target genes, including Lgr5. Partial rescue of this phenotype is achieved by LiCl addition to the culture medium, but not by Wnt agonists. Our results identify Lgr4 as a permissive factor of the Wnt pathway in the intestine and, as such, as a potential target for intestinal cancer therapy.
2012-03-10 | GSE27904 | GEO
Project description:Inevitable need for basement membrane extract (BME) with undefined constituents, such as Matrigel, for intestinal stem cell (ISC) culture in traditional system poses a significant barrier that must be overcome for the development of clinical-grade, scalable, ready-to-use ISCs. Here, we propose a functional polymer-based xenogeneic-free dish for the culture of intestinal stem cells (XF-DISC), ensuring substantially prolonged maintenance of ISCs derived from 3-dimensional human intestinal organoid (ISCs3D-hIO). XF-DISC enables remarkable expandability, exhibiting a 24-fold amplification in cell number within 30 days, with long-term maintenance of ISCs3D-hIO through consecutive passaging more than 30 times (> 210 days), and is fully compatible with a cell banking system. Notably, the ISCs3D-hIO cultured on XF-DISC are successfully transplanted into the intestinal injury and inflammation models, leading to full regeneration of damaged intestinal epithelium. XF-DISC, an extraordinary reliable and scalable xenogeneic-free ISC3D-hIO culture method exhibits significant promise in the development of regenerative ISC therapy for human intestinal diseases.
2024-10-22 | PXD050747 | Pride